In order to get rid of that problem, you must recompile pcsc-lite without the support for LIBHAL. Other problem then arise with for example the fact that the pcsc-lite then doesn't create the /usr/local/pcsc/drivers or /usr/lib/pcsc/drivers directories.

The solution I found was to install the debian packages pcscd and pcsc-omnikey and then to delete the /usr/sbin/pcscd and overwrite it with a compiled version without the libhal support. There are quite some options to give to the ./configure for this, here they are: